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- PDB-5cpf: Compensation of the effect of isoleucine to alanine mutation by d... -

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Basic information

Entry
Database: PDB / ID: 5cpf
TitleCompensation of the effect of isoleucine to alanine mutation by designed inhibition in the InhA enzyme
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Fatty acid biosynthesis inhibition Substrate binding loop conformation Free energy calculation
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / response to antibiotic
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-53K / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.409 Å
AuthorsLi, H.-J. / Lai, C.-T. / Pan, P. / Yu, W. / Shah, S. / Bommineni, G.R. / Perrone, V. / Garcia-Diaz, M. / Tonge, P.J. / Simmerling, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
CitationJournal: Biochemistry / Year: 2015
Title: Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.
Authors: Lai, C.T. / Li, H.J. / Yu, W. / Shah, S. / Bommineni, G.R. / Perrone, V. / Garcia-Diaz, M. / Tonge, P.J. / Simmerling, C.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.country ..._citation.journal_id_CSD / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,82012
Polymers122,7364
Non-polymers4,0838
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18770 Å2
ΔGint-128 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.010, 97.556, 184.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 30684.053 Da / Num. of mol.: 4 / Mutation: I215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: inhA, MT1531 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-53K / 2-(2-methylphenoxy)-5-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]phenol


Mass: 357.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19N3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium Malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 23298 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQ8

2aq8


Resolution: 3.409→48.778 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1195 5.15 %
Rwork0.1819 --
obs0.1854 23208 99.31 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.279 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5836 Å2-0 Å2-0 Å2
2--17.9257 Å20 Å2
3----15.3422 Å2
Refinement stepCycle: LAST / Resolution: 3.409→48.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7718 0 284 0 8002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098182
X-RAY DIFFRACTIONf_angle_d1.37411169
X-RAY DIFFRACTIONf_dihedral_angle_d18.8862978
X-RAY DIFFRACTIONf_chiral_restr0.081235
X-RAY DIFFRACTIONf_plane_restr0.0061428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4087-3.54520.27051330.22072301X-RAY DIFFRACTION95
3.5452-3.70650.28461240.18972422X-RAY DIFFRACTION100
3.7065-3.90180.2621410.18762400X-RAY DIFFRACTION100
3.9018-4.14610.24691360.16772434X-RAY DIFFRACTION100
4.1461-4.4660.20011360.15182448X-RAY DIFFRACTION100
4.466-4.91510.2441060.16412470X-RAY DIFFRACTION100
4.9151-5.62540.27161330.20842460X-RAY DIFFRACTION100
5.6254-7.0840.2971530.20852490X-RAY DIFFRACTION100
7.084-48.7830.21491330.17042588X-RAY DIFFRACTION99

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